1. I have gone with the notion that the older Nekrata (especially the females) are able to develop intelligence enough to communicate much like a great ape etc. Signs, simple noises etc. And their legion enhanced versions even more so who have worked long with their legion handlers so they know hand signals for commands etc. They know the bite of their control necklace even before the painful jolt transmits.

2. Well, its your world, so your call. I would not allow it in my version of the third horizon, but your groups fun is your own.

My first reaction would be why would anyone want to play something so much an abomination to the general populace that any social interaction is impossible? I mean its not even human, then its biosculpted on top of that and even further enhanced with filthy filthy cybernetics! Burn it with fire ! Heresy! Heresy! In my third horizon its a great secret that the Legion uses such beasts and they go to great extent to cover up their usage.

3. Its a feral hunger.. I rule it such that it remains until the beast have fed.4. I would rule no - but once again, its your world. Armor could just be applied to the beast anyhow. The legion Nekrata are cybernetic as is.5. As above, your world.6 *shrug* Infamy rather than reputation and Birr, what would the beast do with Birr? Who would deal and even try to speak with a Nekrata rather than just run away screaming? Its a abomination. More serious note - its your world, if you feel the beasts are accepted then give them the same status and Birr like a refuge perhaps etc.

As it happens, I was thinking of the same thing the other day.
Legion nekatra are beef as hell, hevily augumented and experienced warriors, so playing them is a no go for starting characters. But even with attempt at rolling back from there to something more normal, they are still beefy as hell. So I decided to forget about that and simply see how simplified and balanced I could make a nekatra for player characters.
Here is my first attempt at houserules for nekatra, they might still have too much oomph, but it's a start:

◆THROAT ATTACK:Nekatra often go for the throat of their enemies. A throat attack has a CRIT value of 1 but can only beperformed after the nekatra has spent a fast action to prepare. A successful throat attack pins the nekatra's opponent,who must pass aFORCEtest to break free. For each turnpinned, the victim suffers 1 point of damage and 1 point ofstress.◆FERAL HUNGER: The nekatra enters a state of blind rage, attacking everything around it. It can perform one additional attack perturn at –1, but it can no longer defend itself.